[2023-06-29 06:34:43,911] [INFO] DFAST_QC pipeline started.
[2023-06-29 06:34:43,921] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 06:34:43,921] [INFO] DQC Reference Directory: /var/lib/cwl/stg09679931-3253-429c-b731-8a40cd64c02c/dqc_reference
[2023-06-29 06:34:45,567] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 06:34:45,568] [INFO] Task started: Prodigal
[2023-06-29 06:34:45,569] [INFO] Running command: gunzip -c /var/lib/cwl/stg06ddc749-b7c8-4786-8ec5-fd45958e9e94/GCA_020200475.1_ASM2020047v1_genomic.fna.gz | prodigal -d GCA_020200475.1_ASM2020047v1_genomic.fna/cds.fna -a GCA_020200475.1_ASM2020047v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 06:34:51,604] [INFO] Task succeeded: Prodigal
[2023-06-29 06:34:51,604] [INFO] Task started: HMMsearch
[2023-06-29 06:34:51,604] [INFO] Running command: hmmsearch --tblout GCA_020200475.1_ASM2020047v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09679931-3253-429c-b731-8a40cd64c02c/dqc_reference/reference_markers.hmm GCA_020200475.1_ASM2020047v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 06:34:51,820] [INFO] Task succeeded: HMMsearch
[2023-06-29 06:34:51,821] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg06ddc749-b7c8-4786-8ec5-fd45958e9e94/GCA_020200475.1_ASM2020047v1_genomic.fna.gz]
[2023-06-29 06:34:51,850] [INFO] Query marker FASTA was written to GCA_020200475.1_ASM2020047v1_genomic.fna/markers.fasta
[2023-06-29 06:34:51,850] [INFO] Task started: Blastn
[2023-06-29 06:34:51,850] [INFO] Running command: blastn -query GCA_020200475.1_ASM2020047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09679931-3253-429c-b731-8a40cd64c02c/dqc_reference/reference_markers.fasta -out GCA_020200475.1_ASM2020047v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:34:52,607] [INFO] Task succeeded: Blastn
[2023-06-29 06:34:52,611] [INFO] Selected 14 target genomes.
[2023-06-29 06:34:52,611] [INFO] Target genome list was writen to GCA_020200475.1_ASM2020047v1_genomic.fna/target_genomes.txt
[2023-06-29 06:34:52,612] [INFO] Task started: fastANI
[2023-06-29 06:34:52,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg06ddc749-b7c8-4786-8ec5-fd45958e9e94/GCA_020200475.1_ASM2020047v1_genomic.fna.gz --refList GCA_020200475.1_ASM2020047v1_genomic.fna/target_genomes.txt --output GCA_020200475.1_ASM2020047v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 06:35:01,139] [INFO] Task succeeded: fastANI
[2023-06-29 06:35:01,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09679931-3253-429c-b731-8a40cd64c02c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 06:35:01,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09679931-3253-429c-b731-8a40cd64c02c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 06:35:01,148] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 06:35:01,148] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 06:35:01,148] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	76.94	50	145	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	76.5914	55	145	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	75.8176	50	145	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 06:35:01,150] [INFO] DFAST Taxonomy check result was written to GCA_020200475.1_ASM2020047v1_genomic.fna/tc_result.tsv
[2023-06-29 06:35:01,150] [INFO] ===== Taxonomy check completed =====
[2023-06-29 06:35:01,151] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 06:35:01,151] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09679931-3253-429c-b731-8a40cd64c02c/dqc_reference/checkm_data
[2023-06-29 06:35:01,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 06:35:01,173] [INFO] Task started: CheckM
[2023-06-29 06:35:01,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020200475.1_ASM2020047v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020200475.1_ASM2020047v1_genomic.fna/checkm_input GCA_020200475.1_ASM2020047v1_genomic.fna/checkm_result
[2023-06-29 06:35:24,161] [INFO] Task succeeded: CheckM
[2023-06-29 06:35:24,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.81%
Contamintation: 9.85%
Strain heterogeneity: 83.33%
--------------------------------------------------------------------------------
[2023-06-29 06:35:24,199] [INFO] ===== Completeness check finished =====
[2023-06-29 06:35:24,199] [INFO] ===== Start GTDB Search =====
[2023-06-29 06:35:24,200] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020200475.1_ASM2020047v1_genomic.fna/markers.fasta)
[2023-06-29 06:35:24,200] [INFO] Task started: Blastn
[2023-06-29 06:35:24,200] [INFO] Running command: blastn -query GCA_020200475.1_ASM2020047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09679931-3253-429c-b731-8a40cd64c02c/dqc_reference/reference_markers_gtdb.fasta -out GCA_020200475.1_ASM2020047v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:35:25,503] [INFO] Task succeeded: Blastn
[2023-06-29 06:35:25,508] [INFO] Selected 16 target genomes.
[2023-06-29 06:35:25,509] [INFO] Target genome list was writen to GCA_020200475.1_ASM2020047v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 06:35:25,516] [INFO] Task started: fastANI
[2023-06-29 06:35:25,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg06ddc749-b7c8-4786-8ec5-fd45958e9e94/GCA_020200475.1_ASM2020047v1_genomic.fna.gz --refList GCA_020200475.1_ASM2020047v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020200475.1_ASM2020047v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 06:35:33,665] [INFO] Task succeeded: fastANI
[2023-06-29 06:35:33,667] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 06:35:33,668] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
--------------------------------------------------------------------------------
[2023-06-29 06:35:33,676] [INFO] GTDB search result was written to GCA_020200475.1_ASM2020047v1_genomic.fna/result_gtdb.tsv
[2023-06-29 06:35:33,677] [INFO] ===== GTDB Search completed =====
[2023-06-29 06:35:33,682] [INFO] DFAST_QC result json was written to GCA_020200475.1_ASM2020047v1_genomic.fna/dqc_result.json
[2023-06-29 06:35:33,682] [INFO] DFAST_QC completed!
[2023-06-29 06:35:33,682] [INFO] Total running time: 0h0m50s